I went to Nepal 3 times within last seven months and two times I chose Delhi as a transit point. 

I bought seperate tickets to Delhi and from there to Kathmandu as you are planning to. First time I flew KLM, was in Delhi before midnight. After we landed I went straight to JetAirways transfer desk and showed them my connecting flight ticket, which was for 06:45 (or something like that). They were very helpful and contacted KLM ground staff regarding my baggage. When the KLM guy showed up I gave him my baggage tag. After he signed me as a transit passenger he took me to "pre" transit area and asked me to wait for JetAirways guys. Around 3 am one guy came shouting my name. He wanted my passport, I noted his name and ID number and handed my passport to him. He disappeared for an hour and came back to take me to identify my baggage in front of one custom officer who merely looked at me. Then he handed me my boarding card and I had the security clearence in no time.\\

Second time I flew Turkish Airlines and had a connecting flight to Kathmandu at 12:50 PM with JetAirways. This time they advised me that if I cleared Indian immigration and customs then I wouldn't need to wait in "pre" transit area for 6 hours. I decided to take a chance and was pleasantly surprised at the professional level of Indians at Delhi airport. One question was asked at the immigration and that was regarding my transit arrangement. Went thorugh green channel at the customs and one "babu" stopped me. Threw my baggage in xray and chuckled at "only two" mobiles. Went out, checked in at the JetAirways counter which opens at 0300AM, cleared the security and made myself comfortable at "Delhi Daredevil's" bar for next 6 hours. It was just great.